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Download Article (PDF) DE GRUYTER Journal of Integrative Bioinformatics. 2018; 20180043 Björn Sommer1,2 / Marc Baaden3 / Michael Krone4 / Andrew Woods5 From Virtual Reality to Immersive Analytics in Bioinformatics 1 Computational Life Sciences, Department of Computer and Information Science, University of Konstanz, Konstanz, Germany, E-mail: [email protected] 2 Faculty of Information Technology, Monash University, Melbourne, Australia, E-mail: [email protected] 3 Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France 4 Big Data Visual Analytics, University Tübingen, Tübingen, Germany 5 HIVE (Hub for Immersive Visualisation and eResearch), Curtin University, Perth, Australia Abstract: Bioinformatics-related research produces huge heterogeneous amounts of data. This wealth of information in- cludes data describing metabolic mechanisms and pathways, proteomics, transcriptomics, and metabolomics. Often, the visualization and exploration of related structural – usually molecular – data plays an important role in the aforementioned contexts. For decades, virtual reality (VR)-related technologies were developed and applied to Bioinformatics problems. Often, these approaches provide “just” visual support of the analysis, e.g. in the case of exploring and interacting with a protein on a 3D monitor and compatible interaction hardware. Moreover, in the past these approaches were limited to cost-intensive professional visualization facilities. The advent of new affordable, and often mobile technologies, provides high potential for using similar approaches on a regular basis for daily research. Visual Analytics is successfully being used for several years to analyze com- plex and heterogeneous datasets. Immersive Analytics combines these approaches now with new immersive and interactive technologies. This publication provides a short overview of related technologies, their history and Bioinformatics-related approaches. Six new applications on the path from VR to Immersive Analytics are being introduced and discussed. Keywords: Immersive Analytics, Virtual Reality, Molecular Dynamics, Data Exploration, Cell Modeling and Vi- sualization, Microscopic Imaging, Computational Biology, Semantics DOI: 10.1515/jib-2018-0043 Received: May 29, 2018; Revised: May 29, 2018; Accepted: May 29, 2018 1 Introduction Bioinformatics usually deals with biological macromolecules, the smallest entities of life, therefore, visualiza- tion plays an important role in this field. Stereoscopic rendering has been used for a long time for visualizing biological structures, dating back to the first hype of virtual reality technologies 25 years ago when theCAVE was invented and Head-Mounted Displays (HMD) became affordable. Triggered by the success of new, modern HMDs such as Oculus Rift and HTC Vive, Virtual Reality has recently regained a lot of attention. On the other hand, a new generation of large-scale “computational microscopes” is being established, such as the CAVE2, from River Valley Technologies Ltd representing large, nearly 360 degree-spanning visualization facilities. At the same time, advanced “Visual Analytics” solutions have become an important tool in all areas of scien- tific data analysis, combining visualization, data mining and analysis methods with appropriate user interac- ProofCheck tion. Uniting both VR and VA, “Immersive Analytics” now starts to make use of new technologies, immersing the scientist into the data, and, in the best case, enabling advanced insights. The present manuscript introduces a special issue on these very topics. The special issue comprises six publications: • Interactive Molecular Graphics for Augmented Reality using HoloLens (Section 4.1) • Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell (Section 4.2) Björn Sommer is the corresponding author. ©2018, Björn Sommer et al., published by De Gruyter. Automatically generated rough PDF by This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. 1 Sommer et al. DE GRUYTER • Molecular Dynamics Visualization (MDV): stereoscopic 3D display of biomolecular structure and interac- tions using the Unity game engine (Section 4.3) • Mesoscopic rigid body modelling of the extracellular matrix self-assembly (Section 4.4) • MinOmics, an integrative and immersive tool for multi-omics analysis (Section 4.5) • Semantics for an integrative and immersive pipeline combining visualization and analysis of molecular data (Section 4.6) 1.1 A Workshop with Live and Immersive Demonstrations The special session ’From Virtual Reality to Immersive Analytics in Bioinformatics’ was organized as part of two conferences: Stereoscopic displays and applications (SD&A) XXIX, taking place 29 Jan – 31 Jan 2018, and The engineering reality of virtual reality 2018 (ERVR), taking place 30 Jan – 1 Feb 2018, both in Burlingame, California as part of the 2018 IS&T International Symposium on Electronic Imaging – often just known as the Electronic Imaging Symposium. Established in 1990, and now in its 29th year, SD&A focuses on developments covering the entire stereo- scopic 3D imaging pipeline from capture, processing, and display, to perception. The conference brings together practitioners and researchers from industry and academia to facilitate an exchange of current information on stereoscopic imaging topics. The website is located at: http://stereoscopic.org. The ERVR conference focuses on the creation of virtual and augmented reality systems. In addition to re- search in this area, the trend toward content building continues and practitioners find that technologies and dis- ciplines must be tailored and integrated for specific visualization and interactive applications. This conference serves as a forum where advances and practical advice toward both creative activity and scientific investigation are presented and discussed. Research results as well as applications can be presented. Most of the authors of the manuscripts presented in this contribution provided a live demonstration of their implementation at the conference venue. This demo provided a first hands experience and furthermore enabled us to gauge the public’s enthusiasm for such technologies, which was strong. Furthermore, videos of the implementations were shown, user feedback was described and use cases were reported. Other manuscripts presented at the 2018 SD&A and ERVR conferences will be pub- lished in the Electronic Imaging Symposium conference proceedings available open access at: http://ist.publisher.ingentaconnect.com/content/ist/ei. 2 Virtual Reality in Bioinformatics Virtual Reality-related topics play an important role in many research areas. In philosophy, Plato’s Allegory of the Cave – published in his famous opus Republic – discusses one of the basic principles in discriminating reality, projections and the way the human being relies on his senses to interpret the world. In this way, humans do not see reality, they perceive reality, relying on their senses. Where there is a common denominator for all human beings, there are, of course, strong individual differences, depending on the culture, socialization, and personal experiences. Virtual Reality now extends the projections of the real world to the digital world, an important step in the from River Valley Technologies Ltd quest for the ultimate display [1]. Although the rise of new VR-related technology in the recent years is strongly affiliated to the HMDs such as Oculus Rift® and HTC VIVE® on the visualization side, and to the Leap Motion on the 3D interaction side [2], [3], [4], the ideas behind this technology are not new. The first HMD was de- ProofCheck veloped by Sutherland around 1968 [5]. One of the first approaches to involve multiple senses of a viewer was even developed a few years earlier by Morton Heilig [6]. In the 1980s, the term Virtual Reality became popular, thanks to pioneers like Jaron Lanier, who developed first technological gadgets supporting the 3D visualization and interaction with the computer. The addition of haptics, as demonstrated for biological applications, was an important step [7]. A big breakthrough of the 1990s was the invention of the CAVE®, the Cave Automatic Vir- tual Environment, a visualization system consisting of three to six stereoscopic projection screens, which were installed at many research facilities worldwide [8]. 20 years later, the CAVE2®, a large, nearly 360°-spanning display environment [9], [10], and many other systems around the world are enabling room-scale and group experienced virtual reality. In parallel, the previously mentioned HMDs, such as Oculs Rift, were developed, and alternative devices like the Microsoft HoloLens® support Augmented Reality applications, enabling the projection of 3D scenes into the natural real world environment [11]. Automatically generated rough PDF by 2 DE GRUYTER Sommer et al. In Bioinformatics, many software applications were developed to support VR-related technologies. Obvi- ously, the visualization of the smallest entities of life, not visible to the bare human eye, are one of the appli- cation cases where the use of VR-related technologies is reasonable and promising. Educational software like Meta!Blast, enabling the stereoscopic visualization of cell environments, goes a small step towards this direc- tion [12]. Bryson [13] provides a good overview of scientific applications of this 1990s
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